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Gather and prepare GIS data from data sources

Source: R/gather.R
gather.Rd

Gather raster and vector data from the source (either Google Drive or SFTP), and clip to site boundary, resample and align to standard resolution. Data will be copied from various source locations (orthophotos, DEMs, canopy height models). Robust to crashes and interruptions: cached datasets that are fully downloaded will be used over re-downloading, and processed rasters won't be re-processed unless update = TRUE or replace = TRUE.

Usage

gather(
  site,
  pattern = "",
  update = TRUE,
  check = FALSE,
  field = FALSE,
  resources = NULL,
  local = FALSE,
  trap = TRUE,
  comment = NULL
)

Arguments

site

One or more site names, using 3 letter abbreviation. Use all to process all sites. In batch mode, each named site will be run in a separate job.

pattern

Regex filtering rasters, case-insensitive. Default = "" (match all). Note: only files ending in .tif are included in any case. Examples:

  • to match all Mica orthophotos, use mica_orth

  • to match all Mica files from July, use Jun.*mica

  • to match Mica files for a series of dates, use 11nov20.*mica|14oct20.*mica

update

If TRUE, only process new files, assuming existing files are good; otherwise, process all files and replace existing ones.

check

If TRUE, just check to see that source directories and files exist, but don't cache or process anything

field

If TRUE, download and process the field transects if they don't already exist. The shapefile is downloaded for reference, and a raster corresponding to standard is created.

resources

Slurm launch resources. See launch. These take priority #' over the function's defaults.

local

If TRUE, run locally; otherwise, spawn a batch run on Unity

trap

If TRUE, trap errors in local mode; if FALSE, use normal R error handling. Use this for debugging. If you get unrecovered errors, the job won't be added to the jobs database. Has no effect if local = FALSE.

comment

Optional slurmcollie comment

Details

Additional parameters, set in the gather block in pars.yml (see init()):

  • sourcedrive one of local, google, sftp

    • local - read source from local drive

    • google - get source data from currently connected Google Drive (login via browser on first connection) and cache it locally. Must set cachedir option.

    • sftp - get source data from SFTP site. Must set sftp and cachedir options.

  • sourcedir directory with source rasters, generally on Google Drive or SFTP site

  • subdirs subdirectories to search, ending with slash. Default = orthos, DEMs, and canopy height models (okay to include empty or nonexistent directories). Use <site> in subdirectories that include a site name, e.g., <site> Share/Photogrammetry DEMs. WARNING: paths on the Google Drive are case-sensitive!

  • transects directory with field transect shapefile

  • exclude list of geoTIFFs to exclude, for whatever reasons. Note that files beginning with bad are also excluded

  • sftp list(url = <address of site>, user = <credentials>). Credentials are either username:password or *filename with username:password. Make sure to include credential files in .gitignore and .Rbuildignore so it doesn't end up out in the world!

Source data:

  • geoTIFFs for each site

  • sites file, table of site abbreviation, site name, footprint shapefile, raster standard, and transect shapefile.

Results:

  • flights/geoTIFFs, clipped, resampled, and aligned. Make sure you've closed ArcGIS/QGIS projects that point to these before running!

  • models/gather_data.log

All source data are expected to be in EPSG:4326. Non-conforming rasters will be reprojected.

sites.txt must include the name of the footprint shapefile for each site, a field transect shapefile, and a standard geoTIFF for each site. The footprint is used for clipping and must be present. The transect contains ground truth data, and must be present if field = TRUE. The standard must be present. It is used as the standard for grain and alignment; all rasters will be resampled to match. Standards MUST be in the standard projection, EPSG:4326. Best to use a Mica orthophoto, with 8 cm resolution.

Note that adding to an existing stack using a different standard will lead to sorrow. BEST PRACTICE: don't change the standards in standards.txt; if you must change them, clear the flights/ directory and rerun.

If you're reading from the Google Drive or SFTP, you'll need a cache. Best to put this on the Unity scratch drive. Create it with ws_allocate cache 30 in the Unity shell. You can extend the scratch drive (up to 5 times) with ws_extend cache 30. When you're done with it, be polite and release it with ws_release cache. You'll need to point to the cache in ~/pars.yml, under scratchdir:.

Note that initial runs with Google Drive in a session open the browser for authentication or wait for input from the console, so don't run blindly when using the Google Drive

At the end of a run, the log file will be copied to the flights directory.

Remember that some SFTP servers require connection via VPN

Example runs:

Complete for all sites:

  `gather('all')`

Run for one site, June only:

  `gather(site = 'oth', pattern = 'Jun')`

Run for 2 sites, low tide only:

  `gather(site = c('oth', 'wes'), pattern = '_low_')`